Modules for cell type associate with disease-relevant phenotypes. (a-d) Representative modules for four major cell types - pyramidal neuron (a), astrocyte (b), oligodendrocyte (c), and microglia (d) - each show significant association with a disease-relevant trait. In the first column, module association with region and disease is measured using Bayes ANOVA. Box plots are displayed for each of the four groups (x-axis, labeling as in Figure 2b). In the second column, module association with Braak stage in controls is measured using a t-test. Box plots are displayed for Braak stages (Stg) of 1 and 2. In the third column, Pearson correlation between module expression and age is presented, along with the line of best fit. The y-axis in all cases represents module eigengene expression. P-values: +, 0.05 <P < 0.1; **, P < 0.007; ***, P < 0.0004. In the fourth column, mouse in situ hybridizations for the top hub gene in each module were reproduced from the Allen Mouse Brain Atlas (Allen Institute for Brain Science, ©2009, available from ). These genes appear to mark the appropriate cell types, although no region-specificity is seen in any case. Note that PPAP2B is the top hub gene for a different astrocyte module (light cyan).